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java.lang.Objectuk.ac.sanger.psu.gfmerge.datacomp.GenePredicter
public class GenePredicter
class is representing a geneprediction program (its prediction).
For example:
GenePredicter gp = new GenePredicter(seqOrg, seqComp, predFileName);
Field Summary | |
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private double |
acp
average conditional probability of geneprediction program |
private java.lang.String |
name
name of geneprediction program |
Constructor Summary | |
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GenePredicter(org.biojava.bio.seq.Sequence seqOrg,
org.biojava.bio.seq.Sequence seqComp,
java.lang.String predFileName)
constructor of GenePredicter objects |
Method Summary | |
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private double |
calcAcp(org.biojava.bio.seq.Sequence seqOrg,
org.biojava.bio.seq.Sequence seqComp)
method which retrieves average conditional probability from PredAccuracy object. |
double |
getAcp()
accessor method which returns average conditional probability of genepredicter program. |
java.lang.String |
getName()
accessor method which returns name of genepredicter. |
private java.lang.String |
retrieveName(org.biojava.bio.seq.Sequence seq,
java.lang.String fname)
method which retrieves name of genepredicter program from gene prediction file. |
private void |
setAcp(double _acp)
accessor method which sets average conditional probability of genepredicter program. |
private void |
setName(java.lang.String _name)
accessor method which sets name of genepredicter. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private java.lang.String name
private double acp
Constructor Detail |
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public GenePredicter(org.biojava.bio.seq.Sequence seqOrg, org.biojava.bio.seq.Sequence seqComp, java.lang.String predFileName)
seqOrg
- annotationseqComp
- gene predictionspredFileName
- filename of prediction fileMethod Detail |
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public java.lang.String getName()
private void setName(java.lang.String _name)
_name
- name of genepredicterpublic double getAcp()
PredAccuracy
private void setAcp(double _acp)
_acp
- average conditional probability of genepredicter programPredAccuracy
private java.lang.String retrieveName(org.biojava.bio.seq.Sequence seq, java.lang.String fname)
seq
- sequence which contains BioJava feature with method-tag eachfname
- filename of geneprediction file
private double calcAcp(org.biojava.bio.seq.Sequence seqOrg, org.biojava.bio.seq.Sequence seqComp)
seqOrg
- annotationseqComp
- gene predictions
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